findCellsMod: Modified BRETIGEA findCells() function

In meconsens/CellTyPETool: Facilitates Deconvolution of Bulk Tissue RNAseq Data for Disease Phenotype Analysis

Description

A function that runs BRETIGEA findCells() but returns the used markers

Usage

findCellsMod(inputMat, markers, nMarker, method, scale)

Arguments

inputMat	Numeric gene expression data frame or matrix, with rownames corresponding to gene names, some of which are marker genes, and columns corresponding to samples.
markers	Data frame with marker genes in one column (named "marker") and the cell type that that gene symbol corresponds to in another column (named "cell").
nMarker	The number of marker genes (that are present in your expression data set) to use in estimating the surrogate cell type proportion variable for each cell type.
method	To estimate the cell type proportions, can either use PCA or SVD.
scale	Whether or not to scale the gene expression data from each marker gene prior to using it as an input for dimension reduction.

Value

Returns a list of sample-by-cell type matrix of estimated cell type proportion variables and the markers used

References

#' Chikina M, Zaslavsky E, Sealfon SC. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics . 2015;31(10):1584-91.

Mancarci, B. O., Toker, L., Tripathy, S. J., Li, B., Rocco, B., Sibille, E., & Pavlidis, P. (2017). CrossLaboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. eNeuro, 4(6), ENEURO.0212-17.2017. https://doi.org/10.1523/ENEURO.0212-17.201

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Examples

# Examples 1:
# Using bretCellMarkers, metadata datasets available with package
countDfBret <- countDf
rownames(countDfBret) <- countDfBret$Gene
countDfBret <- countDfBret[,-1]
findCellsModResults <- findCellsMod(
               inputMat = countDfBret,
               markers = bretCellMarkers,
               nMarker = 10,
               method = "SVD",
               scale = TRUE)
findCellsModResults$markerList
findCellsModResults$SPVS

meconsens/CellTyPETool documentation built on Jan. 1, 2021, 9:25 a.m.